Ortega Jesus A, Liang Ziyan, Xu Junpeng Kenny, Gottwein Eva
Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Tarry 6-735, Chicago, IL 60611, USA.
Nucleic Acids Res. 2024 Dec 11;52(22):14171-14183. doi: 10.1093/nar/gkae1103.
MicroRNAs (miRNAs) are pervasive regulators of gene expression, necessitating the development of tools to inhibit individual miRNAs for functional studies or therapeutic targeting. Specialized base-pairing configurations between a miRNA and an RNA target site can trigger the degradation of the targeting miRNA through target-directed miRNA decay (TDMD). Previous work has identified several natural sites that induce TDMD of specific miRNAs. We explored retargeting known TDMD sites for the inhibition of heterologous miRNAs, including several encoded by Kaposi's Sarcoma-associated herpesvirus (KSHV). We focused particularly on miR-K11, a viral mimic of the oncogenic miRNA miR-155. miRNA pairing architectures based on the TDMD site in the long non-coding RNA Cyrano outperformed other retargeted sites. Cyrano-like inhibitors were specific for viral miR-K11 over cellular miR-155 and vice versa. Lentiviral delivery of a Cyrano-like miR-K11 inhibitor into KSHV-transformed primary effusion lymphoma (PEL) cells impaired their viability, showing that miR-K11 promotes KSHV-dependent PEL cell survival. Surprisingly, inactivation of ZSWIM8, a key mediator of TDMD, did not substantially affect miRNA inhibition by retargeted Cyrano-based inhibitors in 293T or PEL cells. Together, our results demonstrate the feasibility of retargeting natural TDMD sites to highly expressed viral or cellular miRNAs and further define features of effective encoded miRNA inhibitors.
微小RNA(miRNA)是基因表达的普遍调节因子,因此需要开发工具来抑制单个miRNA,以进行功能研究或治疗靶向。miRNA与RNA靶位点之间的特殊碱基配对构型可通过靶标导向的miRNA降解(TDMD)触发靶向miRNA的降解。先前的研究已经确定了几个可诱导特定miRNA发生TDMD的天然位点。我们探索了重新利用已知的TDMD位点来抑制异源miRNA,包括由卡波西肉瘤相关疱疹病毒(KSHV)编码的几种miRNA。我们特别关注miR-K11,它是致癌miRNA miR-155的病毒模拟物。基于长链非编码RNA Cyrano中TDMD位点的miRNA配对结构比其他重新靶向的位点表现更优。类似Cyrano的抑制剂对病毒miR-K11具有特异性,而对细胞miR-155则不然,反之亦然。将类似Cyrano的miR-K11抑制剂通过慢病毒导入KSHV转化的原发性渗出性淋巴瘤(PEL)细胞中会损害其活力,这表明miR-K11促进了KSHV依赖性PEL细胞的存活。令人惊讶的是,TDMD的关键介质ZSWIM8的失活并没有显著影响基于Cyrano重新靶向的抑制剂在293T或PEL细胞中对miRNA的抑制作用。总之,我们的结果证明了将天然TDMD位点重新靶向高表达的病毒或细胞miRNA的可行性,并进一步定义了有效编码的miRNA抑制剂的特征。